Cryo-EM structure of stalled rabbit 80S ribosomes in complex with human CCR4-NOT and CNOT4
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8bhf
Q-score: 0.492
Gangwar SP, Yen LY, Yelshanskaya MV, Korman A, Jones DR, Sobolevsky AI
Nat Struct Mol Biol (2023) 30 pp. 1481-1494 [ DOI: doi:10.1038/s41594-023-01080-x Pubmed: 37653241 ]
- 5.8s ribosomal rna (50 kDa, RNA from Oryctolagus cuniculus)
- Nascent chain (501 Da, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l41 (3 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s12 (13 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l21 (18 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s17 (15 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l22 (11 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l26 (15 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein rack1 (34 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l11 (19 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l12 (16 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l23/l25 n-terminal domain-containing protein (13 kDa, Protein from Oryctolagus cuniculus)
- 40s_sa_c domain-containing protein (24 kDa, Protein from Oryctolagus cuniculus)
- Ubiquitin-40s ribosomal protein s27a (7 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s18 (16 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l10 (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s14 (14 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s3a (24 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l36 (11 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s26 (11 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein us15 (17 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l19 (21 kDa, Protein from Oryctolagus cuniculus)
- Ubiquitin-like domain-containing protein (6 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l6 (28 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27 (15 kDa, Protein from Oryctolagus cuniculus)
- Plectin/s10 n-terminal domain-containing protein (11 kDa, Protein from Oryctolagus cuniculus)
- Ubiquitin-60s ribosomal protein l40 (6 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l35a (12 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s11 (17 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l13 (24 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s2 (24 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l5 (34 kDa, Protein from Oryctolagus cuniculus)
- 5s ribosomal rna (38 kDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l14 (16 kDa, Protein from Oryctolagus cuniculus)
- P-site trna (24 kDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l9 (21 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s28 (7 kDa, Protein from Oryctolagus cuniculus)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l37a (10 kDa, Protein from Oryctolagus cuniculus)
- 28s ribosomal rna (1 MDa, RNA from Oryctolagus cuniculus)
- Ribosomal protein l37 (10 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l15 (24 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l13a (23 kDa, Protein from Oryctolagus cuniculus)
- Trash domain-containing protein (12 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l23 (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l18 (21 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l4 (41 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s25 (8 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l29 (13 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l28 (14 kDa, Protein from Oryctolagus cuniculus)
- 18s ribosomal rna (547 kDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l34 (12 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s20 (11 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l35 (14 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s27 (9 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l17 (17 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s5 (21 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27a (16 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s9 (predicted) (21 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l32 (15 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l7 (26 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s16 (16 kDa, Protein from Oryctolagus cuniculus)
- Mrna (896 Da, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l30 (10 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l39-like (6 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l10a (23 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s21 (9 kDa, Protein from Oryctolagus cuniculus)
- Ccr4-not transcription complex subunit 3 (28 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein s19 (15 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s15a (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l36a like (12 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l7a (27 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l31 (12 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l38 (8 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s3 (25 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l8 (26 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s4 (29 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s23 (15 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l18a (20 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s8 (24 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s15 (15 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s7 (21 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s29 (6 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s24 (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l3 (45 kDa, Protein from Oryctolagus cuniculus)
- Ribosome complex (Complex from Oryctolagus cuniculus)
- 60s acidic ribosomal protein p0 (21 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s6 (27 kDa, Protein from Oryctolagus cuniculus)
Human mitochondrial small subunit assembly intermediate (State A)
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 8csp
Q-score: 0.548
Harper NJ, Burnside C, Klinge S
Nature (2023) 614 pp. 175-181 [ DOI: doi:10.1038/s41586-022-05621-0 Pubmed: 36482135 ]
- Potassium ion (39 Da, Ligand)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 28s ribosomal protein s23, mitochondrial (21 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s26, mitochondrial (24 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from Homo sapiens)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Malonyl-coa-acyl carrier protein transacylase, mitochondrial (43 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Homo sapiens)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (78 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s18c, mitochondrial (15 kDa, Protein from Homo sapiens)
- 12s mitochondrial rrna (306 kDa, RNA from Homo sapiens)
- 28s ribosomal protein s10, mitochondrial (23 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s29, mitochondrial (45 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s14, mitochondrial (15 kDa, Protein from Homo sapiens)
- Gtpase era, mitochondrial (48 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Homo sapiens)
- Dimethyladenosine transferase 1, mitochondrial (39 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from Homo sapiens)
- Methyltransferase-like protein 17, mitochondrial (50 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s25, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Homo sapiens)
- Human mitochondrial small subunit assembly intermediate, state a (1 MDa, Complex from Homo sapiens)
- Nitric oxide-associated protein 1 (78 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s9, mitochondrial (45 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s24, mitochondrial (19 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Homo sapiens)
- S-adenosylmethionine (398 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s31, mitochondrial (45 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s17, mitochondrial (14 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s2, mitochondrial (33 kDa, Protein from Homo sapiens)
Human mitochondrial small subunit assembly intermediate (State B)
Resolution: 2.54 Å
EM Method: Single-particle
Fitted PDBs: 8csq
Q-score: 0.566
Harper NJ, Burnside C, Klinge S
Nature (2023) 614 pp. 175-181 [ DOI: doi:10.1038/s41586-022-05621-0 Pubmed: 36482135 ]
- Potassium ion (39 Da, Ligand)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 28s ribosomal protein s23, mitochondrial (21 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s26, mitochondrial (24 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from Homo sapiens)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Malonyl-coa-acyl carrier protein transacylase, mitochondrial (43 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from Homo sapiens)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (78 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s18c, mitochondrial (15 kDa, Protein from Homo sapiens)
- 12s mitochondrial rrna (306 kDa, RNA from Homo sapiens)
- 28s ribosomal protein s10, mitochondrial (23 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s29, mitochondrial (45 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from Homo sapiens)
- Human mitochondrial small subunit assembly intermediate, state b (1 MDa, Complex from Homo sapiens)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s14, mitochondrial (15 kDa, Protein from Homo sapiens)
- Gtpase era, mitochondrial (48 kDa, Protein from Homo sapiens)
- Aurora kinase a-interacting protein (22 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from Homo sapiens)
- Dimethyladenosine transferase 1, mitochondrial (39 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from Homo sapiens)
- Methyltransferase-like protein 17, mitochondrial (50 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s25, mitochondrial (20 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s9, mitochondrial (45 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s24, mitochondrial (19 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from Homo sapiens)
- S-adenosylmethionine (398 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s31, mitochondrial (45 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s17, mitochondrial (14 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from Homo sapiens)
- 28s ribosomal protein s2, mitochondrial (33 kDa, Protein from Homo sapiens)
Human mitochondrial small subunit assembly intermediate (State C)
Resolution: 2.54 Å
EM Method: Single-particle
Fitted PDBs: 8csr
Q-score: 0.563
Harper NJ, Burnside C, Klinge S
Nature (2023) 614 pp. 175-181 [ DOI: doi:10.1038/s41586-022-05621-0 Pubmed: 36482135 ]
- Potassium ion (39 Da, Ligand)
- 28s ribosomal protein s18c, mitochondrial (15 kDa, Protein from human)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 28s ribosomal protein s17, mitochondrial (14 kDa, Protein from human)
- Malonyl-coa-acyl carrier protein transacylase, mitochondrial (43 kDa, Protein from human)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from human)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from human)
- 28s ribosomal protein s23, mitochondrial (21 kDa, Protein from human)
- 28s ribosomal protein s25, mitochondrial (20 kDa, Protein from human)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 28s ribosomal protein s24, mitochondrial (19 kDa, Protein from human)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from human)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from human)
- Zinc ion (65 Da, Ligand)
- 12s mitochondrial rrna (306 kDa, RNA from human)
- Putative ribosome-binding factor a, mitochondrial (38 kDa, Protein from human)
- Water (18 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s10, mitochondrial (23 kDa, Protein from human)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from human)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from human)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from human)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from human)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (78 kDa, Protein from human)
- Methyltransferase-like protein 17, mitochondrial (50 kDa, Protein from human)
- 28s ribosomal protein s2, mitochondrial (33 kDa, Protein from human)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from human)
- 28s ribosomal protein s31, mitochondrial (45 kDa, Protein from human)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from human)
- S-adenosylmethionine (398 Da, Ligand)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from human)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from human)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s14, mitochondrial (15 kDa, Protein from human)
- 28s ribosomal protein s26, mitochondrial (24 kDa, Protein from human)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from human)
- Iron/sulfur cluster (351 Da, Ligand)
- 28s ribosomal protein s29, mitochondrial (45 kDa, Protein from human)
- 28s ribosomal protein s9, mitochondrial (45 kDa, Protein from human)
- Human mitochondrial small subunit assembly intermediate, state c (1 MDa, Complex from Homo sapiens)
- Dimethyladenosine transferase 1, mitochondrial (39 kDa, Protein from human)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from human)
- Aurora kinase a-interacting protein (22 kDa, Protein from human)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from human)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
Human mitochondrial small subunit assembly intermediate (State D)
Resolution: 2.36 Å
EM Method: Single-particle
Fitted PDBs: 8css
Q-score: 0.576
Harper NJ, Burnside C, Klinge S
Nature (2023) 614 pp. 175-181 [ DOI: doi:10.1038/s41586-022-05621-0 Pubmed: 36482135 ]
- Potassium ion (39 Da, Ligand)
- 28s ribosomal protein s18c, mitochondrial (15 kDa, Protein from human)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 28s ribosomal protein s17, mitochondrial (14 kDa, Protein from human)
- Malonyl-coa-acyl carrier protein transacylase, mitochondrial (43 kDa, Protein from human)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from human)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from human)
- 28s ribosomal protein s23, mitochondrial (21 kDa, Protein from human)
- 28s ribosomal protein s25, mitochondrial (20 kDa, Protein from human)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 28s ribosomal protein s24, mitochondrial (19 kDa, Protein from human)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from human)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from human)
- Zinc ion (65 Da, Ligand)
- Putative ribosome-binding factor a, mitochondrial (38 kDa, Protein from human)
- Water (18 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s10, mitochondrial (23 kDa, Protein from human)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from human)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from human)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from human)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from human)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (78 kDa, Protein from human)
- 12s mitochondrial rrna (306 kDa, RNA from human)
- Human mitochondrial small subunit assembly intermediate, state d (1 MDa, Complex from Homo sapiens)
- Methyltransferase-like protein 17, mitochondrial (50 kDa, Protein from human)
- 28s ribosomal protein s2, mitochondrial (33 kDa, Protein from human)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from human)
- 28s ribosomal protein s31, mitochondrial (45 kDa, Protein from human)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from human)
- S-adenosylmethionine (398 Da, Ligand)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from human)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from human)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s14, mitochondrial (15 kDa, Protein from human)
- 28s ribosomal protein s26, mitochondrial (24 kDa, Protein from human)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from human)
- Iron/sulfur cluster (351 Da, Ligand)
- 28s ribosomal protein s29, mitochondrial (45 kDa, Protein from human)
- 28s ribosomal protein s9, mitochondrial (45 kDa, Protein from human)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from human)
- Aurora kinase a-interacting protein (22 kDa, Protein from human)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from human)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
Human mitochondrial small subunit assembly intermediate (State E)
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8cst
Q-score: 0.555
Harper NJ, Burnside C, Klinge S
Nature (2023) 614 pp. 175-181 [ DOI: doi:10.1038/s41586-022-05621-0 Pubmed: 36482135 ]
- Potassium ion (39 Da, Ligand)
- 28s ribosomal protein s18c, mitochondrial (15 kDa, Protein from human)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 28s ribosomal protein s17, mitochondrial (14 kDa, Protein from human)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from human)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from human)
- 28s ribosomal protein s23, mitochondrial (21 kDa, Protein from human)
- 28s ribosomal protein s25, mitochondrial (20 kDa, Protein from human)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 28s ribosomal protein s24, mitochondrial (19 kDa, Protein from human)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from human)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from human)
- Zinc ion (65 Da, Ligand)
- Putative ribosome-binding factor a, mitochondrial (38 kDa, Protein from human)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s10, mitochondrial (23 kDa, Protein from human)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from human)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from human)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from human)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from human)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (78 kDa, Protein from human)
- Human mitochondrial small subunit assembly intermediate, state e (1 MDa, Complex from Homo sapiens)
- 12s mitochondrial rrna (306 kDa, RNA from human)
- Methyltransferase-like protein 17, mitochondrial (50 kDa, Protein from human)
- 28s ribosomal protein s2, mitochondrial (33 kDa, Protein from human)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from human)
- 28s ribosomal protein s31, mitochondrial (45 kDa, Protein from human)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from human)
- S-adenosylmethionine (398 Da, Ligand)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from human)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from human)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s14, mitochondrial (15 kDa, Protein from human)
- 28s ribosomal protein s26, mitochondrial (24 kDa, Protein from human)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from human)
- Iron/sulfur cluster (351 Da, Ligand)
- 28s ribosomal protein s29, mitochondrial (45 kDa, Protein from human)
- 28s ribosomal protein s9, mitochondrial (45 kDa, Protein from human)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from human)
- Aurora kinase a-interacting protein (22 kDa, Protein from human)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from human)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
Human mitochondrial small subunit assembly intermediate (State C*)
Resolution: 3.03 Å
EM Method: Single-particle
Fitted PDBs: 8csu
Q-score: 0.519
Harper NJ, Burnside C, Klinge S
Nature (2023) 614 pp. 175-181 [ DOI: doi:10.1038/s41586-022-05621-0 Pubmed: 36482135 ]
- Potassium ion (39 Da, Ligand)
- 28s ribosomal protein s18c, mitochondrial (15 kDa, Protein from human)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- 28s ribosomal protein s17, mitochondrial (14 kDa, Protein from human)
- 28s ribosomal protein s18b, mitochondrial (29 kDa, Protein from human)
- 28s ribosomal protein s22, mitochondrial (41 kDa, Protein from human)
- 28s ribosomal protein s23, mitochondrial (21 kDa, Protein from human)
- 28s ribosomal protein s25, mitochondrial (20 kDa, Protein from human)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- 28s ribosomal protein s24, mitochondrial (19 kDa, Protein from human)
- 28s ribosomal protein s11, mitochondrial (20 kDa, Protein from human)
- 28s ribosomal protein s27, mitochondrial (47 kDa, Protein from human)
- Human mitochondrial small subunit assembly intermediate, state c* (1 MDa, Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 12s mitochondrial rrna (306 kDa, RNA from human)
- Putative ribosome-binding factor a, mitochondrial (38 kDa, Protein from human)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 28s ribosomal protein s10, mitochondrial (23 kDa, Protein from human)
- 28s ribosomal protein s12, mitochondrial (15 kDa, Protein from human)
- 28s ribosomal protein s6, mitochondrial (14 kDa, Protein from human)
- 28s ribosomal protein s5, mitochondrial (48 kDa, Protein from human)
- 28s ribosomal protein s35, mitochondrial (36 kDa, Protein from human)
- Pentatricopeptide repeat domain-containing protein 3, mitochondrial (78 kDa, Protein from human)
- Methyltransferase-like protein 17, mitochondrial (50 kDa, Protein from human)
- 28s ribosomal protein s2, mitochondrial (33 kDa, Protein from human)
- 28s ribosomal protein s15, mitochondrial (29 kDa, Protein from human)
- 28s ribosomal protein s31, mitochondrial (45 kDa, Protein from human)
- 28s ribosomal protein s7, mitochondrial (28 kDa, Protein from human)
- S-adenosylmethionine (398 Da, Ligand)
- 28s ribosomal protein s33, mitochondrial (12 kDa, Protein from human)
- 28s ribosomal protein s21, mitochondrial (10 kDa, Protein from human)
- Magnesium ion (24 Da, Ligand)
- 28s ribosomal protein s14, mitochondrial (15 kDa, Protein from human)
- 28s ribosomal protein s26, mitochondrial (24 kDa, Protein from human)
- 28s ribosomal protein s28, mitochondrial (20 kDa, Protein from human)
- Iron/sulfur cluster (351 Da, Ligand)
- 28s ribosomal protein s29, mitochondrial (45 kDa, Protein from human)
- 28s ribosomal protein s9, mitochondrial (45 kDa, Protein from human)
- Dimethyladenosine transferase 1, mitochondrial (39 kDa, Protein from human)
- 28s ribosomal protein s16, mitochondrial (15 kDa, Protein from human)
- Aurora kinase a-interacting protein (22 kDa, Protein from human)
- 28s ribosomal protein s34, mitochondrial (25 kDa, Protein from human)
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
Structure of the human 48S initiation complex in open state (h48S AUG open)
Resolution: 4.7 Å
EM Method: Single-particle
Fitted PDBs: 7qp6
Q-score: 0.233
Yi SH, Petrychenko V, Schliep JE, Goyal A, Linden A, Chari A, Urlaub H, Stark H, Rodnina MV, Adio S, Fischer N
Nucleic Acids Res (2022) 50 pp. 5282-5298 [ Pubmed: 35489072 DOI: doi:10.1093/nar/gkac283 ]
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 2 (38 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit a (166 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit e (52 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit c (105 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 1 (36 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 3 (51 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit h (39 kDa, Protein from Homo sapiens)
- Human 48s initiation complex 40s-eif1-eif1a-eif2-eif3-trna-met-mrna (Complex)
- Eukaryotic translation initiation factor 3 subunit m (42 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit g (35 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 1a, x-chromosomal (16 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 1 (12 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- Initiator met-trna-i (24 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s30 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit d (64 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit b (92 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- Mrna (6 kDa, RNA from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit l (66 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- 18s rrna (603 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit k (25 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit f (37 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
Structure of the human 48S initiation complex in closed state (h48S AUG closed)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7qp7
Q-score: 0.337
Yi SH, Petrychenko V, Schliep JE, Goyal A, Linden A, Chari A, Urlaub H, Stark H, Rodnina MV, Adio S, Fischer N
Nucleic Acids Res (2022) 50 pp. 5282-5298 [ Pubmed: 35489072 DOI: doi:10.1093/nar/gkac283 ]
- 40s ribosomal protein s26 (13 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit a (166 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l41 (3 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit e (52 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit c (105 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 1 (36 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 2 subunit 3 (51 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit h (39 kDa, Protein from Homo sapiens)
- Human 48s initiation complex 40s-eif1-eif1a-eif2-eif3-trna-met-mrna (Complex)
- Eukaryotic translation initiation factor 3 subunit m (42 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit g (35 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 1a, x-chromosomal (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- Initiator met-trna-i (24 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- Mrna (82 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s30 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit d (64 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit b (92 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit l (66 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- 18s rrna (603 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit k (25 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- Eukaryotic translation initiation factor 3 subunit f (37 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
Cryo-EM structure of the human SSU processome, state pre-A1
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7mq8
Q-score: 0.417
Singh S, Vanden Broeck A, Miller L, Chaker-Margot M, Klinge S
Science (2021) 373 pp. eabj5338-eabj5338 [ DOI: doi:10.1126/science.abj5338 Pubmed: 34516797 ]
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- Rna cytidine acetyltransferase (115 kDa, Protein from Homo sapiens)
- Periodic tryptophan protein 2 homolog (102 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- Rrna 2'-o-methyltransferase fibrillarin (33 kDa, Protein from Homo sapiens)
- Nucleolar protein 6 (127 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- 5'ets rrna (4 kDa, RNA from Homo sapiens)
- U3 small nucleolar ribonucleoprotein protein imp4 (33 kDa, Protein from Homo sapiens)
- Ribosome biogenesis protein bms1 homolog (145 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- Human ssu processome (5 MDa, Complex from Homo sapiens)
- U3 snorna (70 kDa, RNA from Homo sapiens)
- Wd repeat-containing protein 75 (94 kDa, Protein from Homo sapiens)
- Heat repeat-containing protein 1 (242 kDa, Protein from Homo sapiens)
- Nhp2-like protein 1 (14 kDa, Protein from Homo sapiens)
- Nucleolar protein 56 (66 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- U3 small nucleolar rna-associated protein 15 homolog (58 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 36 (105 kDa, Protein from Homo sapiens)
- Nucleolar protein 14 (68 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (12 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- Bystin (33 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- Nucleolar protein 10 (80 kDa, Protein from Homo sapiens)
- Ribosomal rna-processing protein 7 homolog a (32 kDa, Protein from Homo sapiens)
- Unassigned peptides (23 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Deoxynucleotidyltransferase terminal-interacting protein 2 (84 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- Rrna-processing protein fcf1 homolog (23 kDa, Protein from Homo sapiens)
- Unassigned peptide (3 kDa, Protein from Homo sapiens)
- Transducin beta-like protein 3 (89 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- Rna 3'-terminal phosphate cyclase-like protein (40 kDa, Protein from Homo sapiens)
- Uncharacterized protein c1orf131 (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- Small subunit processome component 20 homolog (318 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- Neuroguidin (35 kDa, Protein from Homo sapiens)
- Krr1 small subunit processome component homolog (43 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- U3 small nucleolar rna-associated protein 18 homolog (62 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- Rrp12-like protein (73 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 46 (68 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-associated protein 14 homolog a (88 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 3 (106 kDa, Protein from Homo sapiens)
- Rna-binding protein pno1 (27 kDa, Protein from Homo sapiens)
- Protein aatf (63 kDa, Protein from Homo sapiens)
- Nucleolar protein 7 (29 kDa, Protein from Homo sapiens)
- U3 small nucleolar ribonucleoprotein protein mpp10 (78 kDa, Protein from Homo sapiens)
- 5'ets rrna (1 MDa, RNA from Homo sapiens)
- U3 small nucleolar rna-associated protein 4 homolog (76 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
- Nucleolar protein 58 (59 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 43 (74 kDa, Protein from Homo sapiens)
- Nucleolar complex protein 4 homolog (50 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- Ribosomal rna small subunit methyltransferase nep1 (26 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- U3 small nucleolar ribonucleoprotein protein imp3 (21 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- Ddb1- and cul4-associated factor 13 (51 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- Nucleolar protein 11 (73 kDa, Protein from Homo sapiens)
- 18s rrna (602 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-interacting protein 2 (51 kDa, Protein from Homo sapiens)
- Probable u3 small nucleolar rna-associated protein 11 (30 kDa, Protein from Homo sapiens)
- U3 small nucleolar rna-associated protein 6 homolog (70 kDa, Protein from Homo sapiens)
- Something about silencing protein 10 (54 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)